Wednesday, July 23, 2014

More Independent Evolution

When a peacock spreads out its train the feathers form a huge display. Near the end of each feather is a colorful, circular object that looks something like an eye and the feathers are positioned just right so that the eyes, or ocelli, are beautifully arrayed across the entire display. The iridescence of the eyes comes not from the material itself, which isn’t colorful, but from its finely-tuned nanostructure which reflects the light to produce the different colors. Such eye-spot feathers are found in three different bird genera and according to a new evolutionary analysis of their genetics, they would likely share a common ancestor as has always been expected by evolutionists. There’s only one problem. The analysis also finds that other bird genera that are without these ornamental eyespots, are also closely related to these genera that do have eye-spot feathers.

If these other genera are so closely related, then why do they not also have ocelli? With evolution we must say that they had the eye-spot feathers but later lost them for some reason, over the course of evolution. Or that the eye-spot feathers evolved independently in the different genera that have them. Either way these are just-so stories, manufactured to fit the theory. As the new study concludes:

The close relationship between taxa with and without ocelli suggests multiple gains or losses. Independent gains, possibly reflecting a pre-existing bias for eye-like structures among females and/or the existence of a simple mutational pathway for the origin of ocelli, appears to be the most likely explanation

This is yet another evidence, in a long, long list, which demonstrates that evolution is not a simple, parsimonious explanation that, in a stroke, easily explains a set of disparate and otherwise unlikely or confusing observations.

Rather, evolution is a complex theory with a never-ending list of epicycles that are needed to explain a wide variety of evidences that are inconsistent with the basic theory. This makes evolution a tautology.

Friday, July 18, 2014

Nothing is Going Right

A new study out of Harvard continues to find problems with the spider evolution story. This time it is a massive genetic study demonstrating that spiders that create orb webs do not fall into the expected evolutionary pattern. As usual, the problem cannot simply be explained away as a consequence of methodological problems and evolutionists are left with convergence or extinction as their only explanations. Either orb weaving evolved multiple times, or it evolved once, proliferated, and then a bunch of species became extinct. Ever since Darwin this denouement has repeated itself over and over—evolutionists apply their theory to a particular problem, their predictions turn out false, and they respond by accommodating the new findings. Skeptics say the theory is failing and evolutionists say this is just good science at work. Did you expect every prediction to be perfect? Inevitably the debate devolves into one over falsification and unfortunately misses what is really important.

There literally are thousands of stories like this spider study. Evolutionary expectations fail, evolutionists adjust and move on, explaining that there’s nothing there that falsified evolution, it was merely a particular prediction that was falsified.

But that doesn’t mean that such failures do not pose serious problems for the theory of evolution. Evolutionists go easy on their theory. They set the bar high and enjoy the ability of their theory to avoid falsification.

To be fair though, one should not expect the practitioners and promoters of a theory to be serious skeptics. Evolutionists sometimes say they would love to falsify their theory, as that would make them famous. But in science there are enormous conformance pressures, ranging from social to monetary. And this is even more so with evolution. If you genuinely question evolution (not just question a sub hypothesis) then you become an anathema. You will be called a creationist. You will be blackballed and rather than becoming famous, you become infamous.

So what is the problem with evolution’s failed predictions, such as this latest study of orb weaving spiders? Actually there are three problems. It is true that the predicted failure, alone, does not falsify evolutionary theory. That’s a rather silly notion given how evolution was never confirmed in the first place, and how flexible is the theory. Evolutionists cannot even explain, in any scientific sense, the evolution of a single protein.

Evolution is metaphysically motivated and has always failed on the science. So the problem is not that new prediction failures falsify the theory. The first problem with such failures is their quantity. There are thousands of such failures. Evolution is consistently coming up short. Its predictions are always wrong and evolutionists are always surprised. To say this steady stream of failure is just a sign of good science is an incredible euphemism.

The second problem with such failures is that they cause the theory to lose parsimony. With each failed prediction, the theory becomes far more complicated as patches and epicycles are added. And this brings us to the third problem, which is related to the second problem.

These failed predictions cause evolution to lose its smoking gun. The strong scientific argument for evolution was that in a stroke it resolves myriad puzzles in the life sciences. There is a consilience across a wide spectrum of disparate disciplines and data, and previously unlikely or bizarre findings are suddenly and simply explained by Darwin’s elegant theory.

This is all a myth as there never was any such genuine consilience. But if one selectively examines the evidence, one can construct such a story. And it is a powerful story. Why do so many species have the pentadactyl structure? It doesn’t seem to make sense, but with common descent it suddenly falls into place. Across those many species, the pentadactyl structure falls neatly into evolution’s common descent pattern. It is all so obvious.

Take this example along with so many others, and you have a consilience. These curious evidences are the smoking gun that compels us to accept evolution. There’s only one problem. There is no such consilience. This latest spider study is just one more example of how the evidence does not fall neatly into the evolutionary pattern—it contradicts that simple, elegant pattern.

Even the venerable pentadactyl structure failed. As Stephen J. Gould put it, “The conclusion seems inescapable, and an old ‘certainty’ must be starkly reversed.”

So it is not that evolutionists cannot explain away all these failures. Of course they can. Evolution is an over-arching, vague, notion that can accommodate myriad findings with all manner of creative explanations. The problem is there is no reason to think, from a scientific perspective, that evolution is a good theory. It cannot explain how the species arose, and the patterns that the species form don’t fit evolution’s expected pattern. There is no smoking gun.

For decades, the story of spider evolution went like this: As insects became more and more diverse, with some species taking to the skies, spiders evolved new hunting strategies, including the ability to weave orb-shaped webs to trap their prey. From that single origin, the story goes, orb-weaver spiders diverged along different evolutionary paths, leading to today, where several species weave similar -- though not identical -- webs. It's a good story, but there's just one problem -- Harvard scientists now know it's not true. The largest-ever phylogenetic study of spiders, conducted by postdoctoral student Rosa Fernández, Gonzalo Giribet, Alexander Agassiz Professor of Zoology, and Gustavo Hormiga, a professor at George Washington University, shows that, contrary to long-held popular opinion, the two groups of spiders that weave orb-shaped webs do not share a single origin.

As the study explains, the findings demand “a major reevaluation of our current understanding of the spider evolutionary chronicle.”

Sunday, July 13, 2014

More Junk DNA That Isn’t Really Junk After All

It is difficult to keep track of all the studies indicating that junk DNA isn’t really junk DNA after all. I have no idea how much actual junk there is in our genomes, but evolution has a long history of failed claims of disutility, inefficiency and junk in nature’s designs. That is why I think Dan Graur took the wrong side of history in his “either the genome is mostly junk or evolution is false” proposition.

A study published last week found strong signs of function in mobile repetitive DNA elements. Mobile genetic elements have been heavily recruited by evolutionists in recent years as powerful, undeniable proofs of common ancestry. An underlying assumption in those proofs, aside from the usual non scientific metaphysics, is that such mobile elements insert themselves into the genome at random. But this study suggests they are at least sometimes nonrandom and functional. As one report explains:

“We’ve come to understand that not all repeat sequences are junk DNA,” said Pawel Michalak, an associate professor at the Virginia Bioinformatics Institute. “These repetitive sequences are increasingly being recognized as agents of adaptive change. We discovered a larger than expected amount of genetic variation in these repeating sequences between the fly populations and saw that the variation resulted in potentially functional differences in important biological processes, such as stress resistance and mating.”

[…]The biological roles of these place-jumping, repetitive elements are mysterious.

They are largely viewed as “genomic parasites,” but in this study, researchers found the mobile DNA can provide genetic novelties recruited as certain population-unique, functional enrichments that are nonrandom and purposeful.

“The first shocker was the sheer volume of genetic variation due to the dynamics of mobile elements, including coding and regulatory genomic regions, and the second was amount of population-specific insertions of transposable DNA elements,” Michalak said. “Roughly 50 percent of the insertions were population unique.”

The fact is, as this study further suggests, we don’t really understand genetics well enough to support the kind of hard claims evolutionists make about the evidence.

Friday, July 11, 2014

Evolutionists Don’t Know What They’re Doing

In Chapter 7 of The Edge of Evolution, Michael Behe explained why protein-protein interactions are a problem for evolution. Here is a summary of the problem. First, protein-protein interactions are important. Proteins often work in teams where half a dozen or more proteins may be interacting with each other to form a molecular machine. Protein-protein interaction is ubiquitous throughout life—so ubiquitous that we now have a name for the collective set of such interactions: the interactome. You can’t do much without protein-protein interactions. It is not as though protein-protein interactions are a convenient extra that makes cells a bit more efficient or bequeaths a few nice-to-have functions. Protein-protein interactions are fundamental to life, and are fundamental at all levels. Evolution must have been creating protein-protein interactions throughout evolutionary history as new species and capabilities arose.

And yet it is difficult to get two proteins to interact in a meaningful way. Such interactions must not be too strong or too weak. Imagine that you had two proteins that you needed to bind meaningfully to each other. If you randomly selected the amino acids at the binding patch on the surface of one of the two proteins, then meaningful binding would be unlikely. In fact, you would have to repeat the experiment millions of times before you could expect to get a good result.

But evolution does not have such resources. It cannot conduct millions of evolutionary experiments in order to luckily find amino acid sequences on protein surfaces that are required for important biological functions. And even if it could, that would only be the first step, because molecular machines are often comprised of multiple proteins, interacting with each other at multiple sites. So evolution would have to luckily find several sequences, in multiple proteins, and get them to arise in similar time frames, so the molecular machine would function.

But that is not all, for molecular machines often work in conjunction with other molecular machines. Having a molecular machine without its neighbors would often not help much.

And yet even with all this there remain more problems. For instance, most proteins are not highly modifiable. You can’t just randomly go about swapping in different amino acids. Protein function typically degrades rapidly with amino acid substitutions. So it is challenging for very much interaction site experimentation to take place in the first place. And of course another problem is that it is astronomically difficult for evolution to evolve a single protein to begin with, let alone meaningful interaction sites.

Simply put, from a scientific perspective protein-protein interaction is another problem for evolution.

Thursday, July 10, 2014

More Biological Fine Tuning

Protein-coding genes provide a sequence of nucleotides that is read three nucleotides at a time. Each triplet is translated into a particular type of amino acid. So a sequence of 300 nucleotides codes for 100 amino acids, which are attached to each other to make a protein. But what if you started not with the first nucleotide in the sequence, but with the second one? You would have a different sequence of nucleotide triplets, and so a different sequence of amino acids. This is also true if you started with the third nucleotide. In fact you could switch over to the opposing DNA strand (the other half of the double helix) and again you would have the choice between three different “frames,” resulting in three different sequences of amino acids. So in all you can choose between six different reading frames. So any given gene has the theoretical possibility of containing different genetic messages, in the different reading frames. And indeed, years ago it was discovered that genes are overlapping—portions of their nucleotide sequence exist on the same segment of DNA, just in a different reading frame. But an even more bizarre theoretical possibility is that the reading frame could shift while the sequence of nucleotides is being read. In that case you are mixing and matching partial sequences from different reading frames. Now, a new study has investigated this capability and discovered a fascinating mechanism that apparently enables the real-time frame shifting.

Nucleotide sequences are translated into amino acid sequences at the cell’s ribosome structures and the new study found that this translation process can be programmed to skip a nucleotide, and so switch to another reading frame, attaching two short snippets of nucleotide segments, known as microRNAs, to the main nucleotide sequence at certain locations. The study suggests that a pseudoknot, or triplex, RNA structure is formed causing the skip to occur. Of course the right nucleotide sequence is required, and the right microRNA sequences are required. It was not easy to solve this complicated puzzle, as one researcher explained:

These are really complex RNA structures. It takes a lot of computer memory to search for them in human cells. It wasn’t until the past decade that computers were fast and powerful enough to find these signals.

It is yet another “novel mode” of realtime biological response resulting in “fine-tuned” cell performance. It all just smacks of random mutations.